LOINC
Version 2.72

100157-7SARS-CoV-2 (COVID-19) lineage [Type] in Specimen by SequencingActive

Term Description

SARS coronavirus 2 (SARS-CoV-2) lineage result based on a sequencing study. Results may be determined using the Pangolin lineage assignment application [https://cov-lineages.org/pangolin.html].
Source: Regenstrief LOINC

Part Descriptions

LP422739-5   SARS coronavirus 2 lineage
Lineage nomenclatures are intended to provide a detailed level differentiation of viral mutations of SARS-CoV-2 over time. However, proposed lineage nomenclatures are not intended to portray every evolutionary change, but rather those associated with important epidemiological and biological events.[PMID:32669681] That being said they are not as broad-brushed as clades, but are expected to correspond to outbreaks.[PMID:32794443] Source: Regenstrief LOINC

LP150045-5   Sequencing
Sequencing is a method used to determine the sequence of individual genes, larger genetic regions (i.e. clusters of genes or operons), full chromosomes or entire genomes. Historically, most sequencing has been performed using the chain termination method developed by Frederick Sanger in 1977.[PMID:271968] Sequencing technologies have improved dramatically, making them cheaper, faster, and more accurate. Next-generation sequencing (NGS), also known as high-throughput sequencing, deep sequencing, and second-generation sequencing, is a type of technology that uses parallel sequencing of multiple small fragments of DNA to determine sequence. This "high-throughput" technology has increased the speed and amount of DNA sequenced at a significantly reduced cost.[PMID:18576944] Several NGS platforms (ie, sequencing instruments and associated reagents) have been developed. Third-generation sequencing is another methodology currently under development that uses parallel sequencing similar to NGS. In contrast to NGS, third-generation sequencing uses single DNA molecules rather than amplified DNA as a template.[PMID:20858600] Source: Regenstrief LOINC

Fully-Specified Name

Component
SARS coronavirus 2 lineage
Property
Type
Time
Pt
System
XXX
Scale
Nom
Method
Sequencing

Additional Names

Short Name
SARS-CoV-2 lineage Spec Seq
Display Name
SARS-CoV-2 (COVID-19) lineage Sequencing Nom (Specimen)
Consumer Name Alpha
SARS-CoV-2 (COVID-19) lineage, Specimen

Example Answer List LL5807-4

Source: LOINC

Answer Code Score Answer ID
SARS-CoV-2 A.1.1 lineage LA31701-8
SARS-CoV-2 B.1.1.238 lineage

Also known as Nigerian variant

LA31620-0
SARS-CoV-2 B.1.2 lineage LA31703-4
SARS-CoV-2 B.1.1 lineage LA31704-2
SARS-CoV-2 B.1.1.7 lineage

Also known as WHO Alpha variant, and UK variant

LA31705-9
SARS-CoV-2 B.1.29 lineage LA31706-7
SARS-CoV-2 B.2.4 lineage LA31702-6
SARS-CoV-2 B.1.351 lineage

Also known as WHO Beta variant, GH/501Y.V2, and South Africa variant

LA32553-2
SARS-CoV-2 P.1 lineage

Also known as WHO gamma lineage, and Brazil variant

LA32555-7
SARS-CoV-2 B.1.617.2 lineage

Also known as WHO Delta variant

LA32556-5

Basic Attributes

Class
MICRO
Type
Laboratory
First Released
Version 2.72
Last Updated
Version 2.72
Order vs. Observation
Both

Member of these Groups

LG51017-8 SARSCoV2 detection
LG51019-4 SARSCoV2 molecular detection

Language Variants Get Info

zh-CNChinese (China)
SARS 冠状病毒 2 谱系:类型:时间点:XXX:名义型:序列测定
nl-NLDutch (Netherlands)
SARS-CoV-2 lineage:type:moment:XXX:nominaal:sequencing
it-ITItalian (Italy)
SARS coronavirus 2, lignaggio:Tipo:Pt:XXX:Nom:Sequenziamento
pl-PLPolish (Poland)
linia rodowodowa SARS-CoV-2:Typ:Punkt w czasie:XXX:Nominalny:Sekwencjonowanie
es-ESSpanish (Spain)
Linaje de SARS-CoV-2 (COVID-19):Tipo:Punto temporal:XXX:Nom:Secuenciación

LOINC FHIR® API Example - CodeSystem Request Get Info

https://fhir.loinc.org/CodeSystem/$lookup?system=http://loinc.org&code=100157-7